@Joe Villeneuve
The point is some projects justify a full replacement, and some do not. While 'most' of the time it may make sense to pull the trigger on a full roof replacement (or perhaps a furnace replacement) all at once, it will depend on the circumstances. I think it's not wise to advocate always doing so, for multiple reasons, a few already pointed out.
I can come up with specific circumstances where we can all agree a full furnace replacement wouldn't make sense and I can also come up with specific circumstances where a full roof replacement wouldn't make sense.
@Jim Young
With the above said, it seems you stated that most of the roof is towards the end of its life. If operating capital is not of a primary concern/constraint, then I think you're right to consider tax treatments of a partial vs. full solution. I can't speak to that but I'd think that's a secondary consideration to the below (at least how I'd approach it, anyways).
I think since cash/operating capital is not a primary consideration, it is good to consider that a good chunk of the costs (and therefore price) associated with a project like this is getting the crew mobilized to do the work, and you may end up 'double paying' for some of that.
The other consideration I can think of against doing the half roof is just the shingle matching aspect. Even though you stated that you can't see both at once, if they aren't a perfect match, you get into the aesthetic look over time that just might look 'patched together.' Even the difference in age may make the weathering look different for the different parts of the roof. This may affect your asset's ability to hold value (real or perceived) over time, perhaps (low risk) for appraisals for refinances, etc - but (higher risk) during a more in depth diligence/inspection when you're selling.